Multiple sequence alignment - TraesCS4B01G108500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G108500 chr4B 100.000 3108 0 0 1 3108 119309214 119312321 0.000000e+00 5740
1 TraesCS4B01G108500 chr4B 97.826 138 3 0 2971 3108 475713773 475713636 4.010000e-59 239
2 TraesCS4B01G108500 chr3B 96.973 2015 46 1 961 2975 11908418 11910417 0.000000e+00 3369
3 TraesCS4B01G108500 chr3B 93.398 1545 79 11 1432 2975 725543909 725545431 0.000000e+00 2266
4 TraesCS4B01G108500 chr3B 95.277 974 40 6 1 971 816950556 816949586 0.000000e+00 1539
5 TraesCS4B01G108500 chr3B 94.995 979 43 6 1 976 681874781 681875756 0.000000e+00 1531
6 TraesCS4B01G108500 chr3B 94.518 456 16 6 970 1421 725543292 725543742 0.000000e+00 695
7 TraesCS4B01G108500 chr3B 97.826 138 3 0 2971 3108 656574210 656574073 4.010000e-59 239
8 TraesCS4B01G108500 chr3B 94.702 151 6 2 2958 3108 72136408 72136260 1.860000e-57 233
9 TraesCS4B01G108500 chr3B 94.000 100 6 0 2293 2392 725544828 725544927 5.370000e-33 152
10 TraesCS4B01G108500 chr7B 96.328 2015 47 1 961 2975 320266061 320264074 0.000000e+00 3286
11 TraesCS4B01G108500 chr7B 98.439 961 13 2 1 960 182382126 182381167 0.000000e+00 1690
12 TraesCS4B01G108500 chr7B 87.906 1323 93 35 1432 2704 66321857 66323162 0.000000e+00 1495
13 TraesCS4B01G108500 chr7B 95.687 881 35 2 1435 2314 733294389 733293511 0.000000e+00 1413
14 TraesCS4B01G108500 chr7B 91.508 683 45 3 2293 2975 733270279 733269610 0.000000e+00 928
15 TraesCS4B01G108500 chr1B 95.231 1405 49 3 1572 2975 176794328 176792941 0.000000e+00 2207
16 TraesCS4B01G108500 chr1B 95.630 961 39 3 1 960 493195971 493196929 0.000000e+00 1539
17 TraesCS4B01G108500 chr1B 86.253 1113 80 37 1887 2975 61977957 61979020 0.000000e+00 1140
18 TraesCS4B01G108500 chr1B 94.783 460 23 1 961 1420 61968279 61968737 0.000000e+00 715
19 TraesCS4B01G108500 chr1B 93.856 472 26 2 961 1430 176803413 176802943 0.000000e+00 708
20 TraesCS4B01G108500 chr6B 90.242 1568 88 39 1432 2975 114059061 114060587 0.000000e+00 1988
21 TraesCS4B01G108500 chr6B 96.154 962 33 4 1 960 428378729 428379688 0.000000e+00 1568
22 TraesCS4B01G108500 chr6B 95.950 963 35 4 1 961 428371301 428372261 0.000000e+00 1559
23 TraesCS4B01G108500 chr6B 95.946 962 35 3 1 960 537115167 537116126 0.000000e+00 1557
24 TraesCS4B01G108500 chr6B 95.652 460 20 0 961 1420 114058461 114058920 0.000000e+00 739
25 TraesCS4B01G108500 chr3D 89.347 1577 99 36 1441 2975 580651263 580649714 0.000000e+00 1917
26 TraesCS4B01G108500 chr3D 88.642 1576 115 26 1432 2975 155676799 155678342 0.000000e+00 1860
27 TraesCS4B01G108500 chr3D 90.000 480 35 5 961 1434 447609514 447609042 2.650000e-170 608
28 TraesCS4B01G108500 chr1D 88.819 1583 95 39 1435 2975 422849839 422848297 0.000000e+00 1868
29 TraesCS4B01G108500 chr2D 87.101 1597 119 47 1432 2975 77210533 77212095 0.000000e+00 1727
30 TraesCS4B01G108500 chr5B 95.963 966 33 6 1 961 286469715 286468751 0.000000e+00 1563
31 TraesCS4B01G108500 chr5B 95.859 966 34 6 1 961 286477162 286476198 0.000000e+00 1557
32 TraesCS4B01G108500 chr5B 87.194 695 50 10 2287 2975 659492180 659492841 0.000000e+00 754
33 TraesCS4B01G108500 chr2B 93.636 990 52 8 1435 2423 765113872 765112893 0.000000e+00 1469
34 TraesCS4B01G108500 chr2B 89.751 683 52 5 2293 2975 765112956 765112292 0.000000e+00 857
35 TraesCS4B01G108500 chr2B 92.208 462 28 6 970 1426 765114495 765114037 0.000000e+00 647
36 TraesCS4B01G108500 chr2B 91.411 163 10 4 2947 3107 114368306 114368146 1.450000e-53 220
37 TraesCS4B01G108500 chr2B 94.000 100 6 0 2293 2392 765112897 765112798 5.370000e-33 152
38 TraesCS4B01G108500 chr4A 89.137 672 53 10 2306 2975 37982975 37982322 0.000000e+00 819
39 TraesCS4B01G108500 chr5A 89.004 673 53 11 2306 2975 509130520 509131174 0.000000e+00 813
40 TraesCS4B01G108500 chr6A 89.074 659 51 11 2320 2975 532334409 532333769 0.000000e+00 798
41 TraesCS4B01G108500 chr5D 90.566 477 35 5 961 1434 504761743 504762212 9.460000e-175 623
42 TraesCS4B01G108500 chrUn 97.826 138 3 0 2971 3108 2856548 2856411 4.010000e-59 239
43 TraesCS4B01G108500 chrUn 97.826 138 3 0 2971 3108 395081256 395081119 4.010000e-59 239
44 TraesCS4B01G108500 chrUn 97.826 138 3 0 2971 3108 415448740 415448877 4.010000e-59 239
45 TraesCS4B01G108500 chrUn 97.826 138 3 0 2971 3108 424251666 424251803 4.010000e-59 239
46 TraesCS4B01G108500 chrUn 97.826 138 3 0 2971 3108 427324280 427324417 4.010000e-59 239


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G108500 chr4B 119309214 119312321 3107 False 5740.000000 5740 100.00000 1 3108 1 chr4B.!!$F1 3107
1 TraesCS4B01G108500 chr3B 11908418 11910417 1999 False 3369.000000 3369 96.97300 961 2975 1 chr3B.!!$F1 2014
2 TraesCS4B01G108500 chr3B 816949586 816950556 970 True 1539.000000 1539 95.27700 1 971 1 chr3B.!!$R3 970
3 TraesCS4B01G108500 chr3B 681874781 681875756 975 False 1531.000000 1531 94.99500 1 976 1 chr3B.!!$F2 975
4 TraesCS4B01G108500 chr3B 725543292 725545431 2139 False 1037.666667 2266 93.97200 970 2975 3 chr3B.!!$F3 2005
5 TraesCS4B01G108500 chr7B 320264074 320266061 1987 True 3286.000000 3286 96.32800 961 2975 1 chr7B.!!$R2 2014
6 TraesCS4B01G108500 chr7B 182381167 182382126 959 True 1690.000000 1690 98.43900 1 960 1 chr7B.!!$R1 959
7 TraesCS4B01G108500 chr7B 66321857 66323162 1305 False 1495.000000 1495 87.90600 1432 2704 1 chr7B.!!$F1 1272
8 TraesCS4B01G108500 chr7B 733293511 733294389 878 True 1413.000000 1413 95.68700 1435 2314 1 chr7B.!!$R4 879
9 TraesCS4B01G108500 chr7B 733269610 733270279 669 True 928.000000 928 91.50800 2293 2975 1 chr7B.!!$R3 682
10 TraesCS4B01G108500 chr1B 176792941 176794328 1387 True 2207.000000 2207 95.23100 1572 2975 1 chr1B.!!$R1 1403
11 TraesCS4B01G108500 chr1B 493195971 493196929 958 False 1539.000000 1539 95.63000 1 960 1 chr1B.!!$F3 959
12 TraesCS4B01G108500 chr1B 61977957 61979020 1063 False 1140.000000 1140 86.25300 1887 2975 1 chr1B.!!$F2 1088
13 TraesCS4B01G108500 chr6B 428378729 428379688 959 False 1568.000000 1568 96.15400 1 960 1 chr6B.!!$F2 959
14 TraesCS4B01G108500 chr6B 428371301 428372261 960 False 1559.000000 1559 95.95000 1 961 1 chr6B.!!$F1 960
15 TraesCS4B01G108500 chr6B 537115167 537116126 959 False 1557.000000 1557 95.94600 1 960 1 chr6B.!!$F3 959
16 TraesCS4B01G108500 chr6B 114058461 114060587 2126 False 1363.500000 1988 92.94700 961 2975 2 chr6B.!!$F4 2014
17 TraesCS4B01G108500 chr3D 580649714 580651263 1549 True 1917.000000 1917 89.34700 1441 2975 1 chr3D.!!$R2 1534
18 TraesCS4B01G108500 chr3D 155676799 155678342 1543 False 1860.000000 1860 88.64200 1432 2975 1 chr3D.!!$F1 1543
19 TraesCS4B01G108500 chr1D 422848297 422849839 1542 True 1868.000000 1868 88.81900 1435 2975 1 chr1D.!!$R1 1540
20 TraesCS4B01G108500 chr2D 77210533 77212095 1562 False 1727.000000 1727 87.10100 1432 2975 1 chr2D.!!$F1 1543
21 TraesCS4B01G108500 chr5B 286468751 286469715 964 True 1563.000000 1563 95.96300 1 961 1 chr5B.!!$R1 960
22 TraesCS4B01G108500 chr5B 286476198 286477162 964 True 1557.000000 1557 95.85900 1 961 1 chr5B.!!$R2 960
23 TraesCS4B01G108500 chr5B 659492180 659492841 661 False 754.000000 754 87.19400 2287 2975 1 chr5B.!!$F1 688
24 TraesCS4B01G108500 chr2B 765112292 765114495 2203 True 781.250000 1469 92.39875 970 2975 4 chr2B.!!$R2 2005
25 TraesCS4B01G108500 chr4A 37982322 37982975 653 True 819.000000 819 89.13700 2306 2975 1 chr4A.!!$R1 669
26 TraesCS4B01G108500 chr5A 509130520 509131174 654 False 813.000000 813 89.00400 2306 2975 1 chr5A.!!$F1 669
27 TraesCS4B01G108500 chr6A 532333769 532334409 640 True 798.000000 798 89.07400 2320 2975 1 chr6A.!!$R1 655

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
623 633 0.257039 CCCTGGCTATTGTCTTGGCT 59.743 55.000 0.00 0.0 0.00 4.75 F
1172 1187 2.199208 TGGATTTCTCAGATCCCAGCA 58.801 47.619 1.03 0.0 41.97 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 1916 4.096231 CCACACACACTGAAATGTTCTCAA 59.904 41.667 0.0 0.0 0.00 3.02 R
2975 3494 0.394488 TTCTGCAACGTTCCCCAACA 60.394 50.000 0.0 0.0 32.14 3.33 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
321 328 6.075315 ACTGTGGTATTTCTTTTAAAGCCCT 58.925 36.000 0.00 0.00 0.00 5.19
365 373 2.607771 CCCGACTGTGGCATTCTTTTTG 60.608 50.000 0.00 0.00 0.00 2.44
623 633 0.257039 CCCTGGCTATTGTCTTGGCT 59.743 55.000 0.00 0.00 0.00 4.75
727 737 2.706190 AGTTAACCTGGTCAGCTGTTCT 59.294 45.455 14.67 0.00 0.00 3.01
976 988 4.067512 AGCTCGCTCCCCTCTCCA 62.068 66.667 0.00 0.00 0.00 3.86
987 999 3.125573 CTCTCCAGTCGCCGTCGA 61.126 66.667 0.00 0.00 43.28 4.20
1127 1141 4.909088 TCTAGGGTTTCTAGGGTTCAACAA 59.091 41.667 0.00 0.00 44.29 2.83
1172 1187 2.199208 TGGATTTCTCAGATCCCAGCA 58.801 47.619 1.03 0.00 41.97 4.41
1421 1464 5.989477 TGTTCATGTTCTAGGGTTCATAGG 58.011 41.667 0.00 0.00 0.00 2.57
1716 1916 7.056635 CCTGAGGTAAACCATAAGAATGATGT 58.943 38.462 1.26 0.00 38.89 3.06
2474 2962 2.797156 GGCATGCTAACATACTGACGAG 59.203 50.000 18.92 0.00 33.67 4.18
2493 2981 6.594159 TGACGAGACTGAACTTTTTCTTCTTT 59.406 34.615 0.00 0.00 32.36 2.52
2700 3204 4.312443 CAGCAGCTTTTCCACATCAATTT 58.688 39.130 0.00 0.00 0.00 1.82
2757 3261 0.108186 CGCCAGGAGCTACACATCAA 60.108 55.000 0.00 0.00 40.39 2.57
2975 3494 3.352338 GAGGACGGCGTCGGTGATT 62.352 63.158 31.02 13.54 41.39 2.57
2976 3495 3.186047 GGACGGCGTCGGTGATTG 61.186 66.667 31.02 0.00 41.39 2.67
2977 3496 2.431942 GACGGCGTCGGTGATTGT 60.432 61.111 25.42 0.00 41.39 2.71
2978 3497 2.025418 GACGGCGTCGGTGATTGTT 61.025 57.895 25.42 0.00 41.39 2.83
2979 3498 2.222953 GACGGCGTCGGTGATTGTTG 62.223 60.000 25.42 0.00 41.39 3.33
2980 3499 2.867472 GGCGTCGGTGATTGTTGG 59.133 61.111 0.00 0.00 0.00 3.77
2981 3500 2.686816 GGCGTCGGTGATTGTTGGG 61.687 63.158 0.00 0.00 0.00 4.12
2982 3501 2.686816 GCGTCGGTGATTGTTGGGG 61.687 63.158 0.00 0.00 0.00 4.96
2983 3502 1.004320 CGTCGGTGATTGTTGGGGA 60.004 57.895 0.00 0.00 0.00 4.81
2984 3503 0.604243 CGTCGGTGATTGTTGGGGAA 60.604 55.000 0.00 0.00 0.00 3.97
2985 3504 0.879090 GTCGGTGATTGTTGGGGAAC 59.121 55.000 0.00 0.00 0.00 3.62
2986 3505 0.604243 TCGGTGATTGTTGGGGAACG 60.604 55.000 0.00 0.00 0.00 3.95
2987 3506 0.887387 CGGTGATTGTTGGGGAACGT 60.887 55.000 0.00 0.00 0.00 3.99
2988 3507 1.324383 GGTGATTGTTGGGGAACGTT 58.676 50.000 0.00 0.00 0.00 3.99
2989 3508 1.000717 GGTGATTGTTGGGGAACGTTG 60.001 52.381 5.00 0.00 0.00 4.10
2990 3509 0.671251 TGATTGTTGGGGAACGTTGC 59.329 50.000 11.85 11.85 0.00 4.17
2991 3510 0.671251 GATTGTTGGGGAACGTTGCA 59.329 50.000 21.74 0.00 0.00 4.08
2992 3511 0.673437 ATTGTTGGGGAACGTTGCAG 59.327 50.000 21.74 0.00 0.00 4.41
2993 3512 0.394488 TTGTTGGGGAACGTTGCAGA 60.394 50.000 21.74 3.97 0.00 4.26
2994 3513 0.394488 TGTTGGGGAACGTTGCAGAA 60.394 50.000 21.74 10.10 0.00 3.02
2995 3514 0.741915 GTTGGGGAACGTTGCAGAAA 59.258 50.000 21.74 9.26 0.00 2.52
2996 3515 1.135333 GTTGGGGAACGTTGCAGAAAA 59.865 47.619 21.74 6.84 0.00 2.29
2997 3516 1.698506 TGGGGAACGTTGCAGAAAAT 58.301 45.000 21.74 0.00 0.00 1.82
2998 3517 2.035632 TGGGGAACGTTGCAGAAAATT 58.964 42.857 21.74 0.00 0.00 1.82
2999 3518 3.223435 TGGGGAACGTTGCAGAAAATTA 58.777 40.909 21.74 0.00 0.00 1.40
3000 3519 3.637229 TGGGGAACGTTGCAGAAAATTAA 59.363 39.130 21.74 0.00 0.00 1.40
3001 3520 4.099573 TGGGGAACGTTGCAGAAAATTAAA 59.900 37.500 21.74 0.00 0.00 1.52
3002 3521 5.051153 GGGGAACGTTGCAGAAAATTAAAA 58.949 37.500 21.74 0.00 0.00 1.52
3003 3522 5.699001 GGGGAACGTTGCAGAAAATTAAAAT 59.301 36.000 21.74 0.00 0.00 1.82
3004 3523 6.203915 GGGGAACGTTGCAGAAAATTAAAATT 59.796 34.615 21.74 0.00 0.00 1.82
3005 3524 7.254966 GGGGAACGTTGCAGAAAATTAAAATTT 60.255 33.333 21.74 0.00 40.15 1.82
3007 3526 9.497030 GGAACGTTGCAGAAAATTAAAATTTTT 57.503 25.926 15.52 0.00 45.70 1.94
3009 3528 9.497030 AACGTTGCAGAAAATTAAAATTTTTCC 57.503 25.926 9.06 3.98 45.70 3.13
3010 3529 8.888716 ACGTTGCAGAAAATTAAAATTTTTCCT 58.111 25.926 9.06 5.83 45.70 3.36
3014 3533 8.983724 TGCAGAAAATTAAAATTTTTCCTACGG 58.016 29.630 9.06 4.45 45.70 4.02
3015 3534 8.984764 GCAGAAAATTAAAATTTTTCCTACGGT 58.015 29.630 9.06 0.00 45.70 4.83
3021 3540 8.821147 ATTAAAATTTTTCCTACGGTTTCACC 57.179 30.769 9.06 0.00 34.05 4.02
3022 3541 5.855740 AAATTTTTCCTACGGTTTCACCA 57.144 34.783 0.00 0.00 38.47 4.17
3023 3542 5.855740 AATTTTTCCTACGGTTTCACCAA 57.144 34.783 0.00 0.00 38.47 3.67
3024 3543 5.855740 ATTTTTCCTACGGTTTCACCAAA 57.144 34.783 0.00 0.00 38.47 3.28
3025 3544 5.656213 TTTTTCCTACGGTTTCACCAAAA 57.344 34.783 0.00 0.00 38.47 2.44
3026 3545 5.855740 TTTTCCTACGGTTTCACCAAAAT 57.144 34.783 0.00 0.00 38.47 1.82
3027 3546 5.441709 TTTCCTACGGTTTCACCAAAATC 57.558 39.130 0.00 0.00 38.47 2.17
3028 3547 3.414269 TCCTACGGTTTCACCAAAATCC 58.586 45.455 0.00 0.00 38.47 3.01
3029 3548 3.150767 CCTACGGTTTCACCAAAATCCA 58.849 45.455 0.00 0.00 38.47 3.41
3030 3549 3.761752 CCTACGGTTTCACCAAAATCCAT 59.238 43.478 0.00 0.00 38.47 3.41
3031 3550 3.934457 ACGGTTTCACCAAAATCCATC 57.066 42.857 0.00 0.00 38.47 3.51
3032 3551 3.496331 ACGGTTTCACCAAAATCCATCT 58.504 40.909 0.00 0.00 38.47 2.90
3033 3552 4.658063 ACGGTTTCACCAAAATCCATCTA 58.342 39.130 0.00 0.00 38.47 1.98
3034 3553 5.261216 ACGGTTTCACCAAAATCCATCTAT 58.739 37.500 0.00 0.00 38.47 1.98
3035 3554 5.125417 ACGGTTTCACCAAAATCCATCTATG 59.875 40.000 0.00 0.00 38.47 2.23
3036 3555 5.356751 CGGTTTCACCAAAATCCATCTATGA 59.643 40.000 0.00 0.00 38.47 2.15
3037 3556 6.458751 CGGTTTCACCAAAATCCATCTATGAG 60.459 42.308 0.00 0.00 38.47 2.90
3038 3557 6.378280 GGTTTCACCAAAATCCATCTATGAGT 59.622 38.462 0.00 0.00 38.42 3.41
3039 3558 7.093771 GGTTTCACCAAAATCCATCTATGAGTT 60.094 37.037 0.00 0.00 38.42 3.01
3040 3559 7.630242 TTCACCAAAATCCATCTATGAGTTC 57.370 36.000 0.00 0.00 0.00 3.01
3041 3560 6.720309 TCACCAAAATCCATCTATGAGTTCA 58.280 36.000 0.00 0.00 0.00 3.18
3042 3561 7.348815 TCACCAAAATCCATCTATGAGTTCAT 58.651 34.615 0.00 0.00 40.22 2.57
3043 3562 7.500227 TCACCAAAATCCATCTATGAGTTCATC 59.500 37.037 0.00 0.00 37.76 2.92
3044 3563 7.501559 CACCAAAATCCATCTATGAGTTCATCT 59.498 37.037 0.00 0.00 37.76 2.90
3045 3564 8.717717 ACCAAAATCCATCTATGAGTTCATCTA 58.282 33.333 0.00 0.00 37.76 1.98
3046 3565 9.565090 CCAAAATCCATCTATGAGTTCATCTAA 57.435 33.333 0.00 0.00 37.76 2.10
3048 3567 8.845413 AAATCCATCTATGAGTTCATCTAAGC 57.155 34.615 0.00 0.00 37.76 3.09
3049 3568 6.983906 TCCATCTATGAGTTCATCTAAGCA 57.016 37.500 0.00 0.00 37.76 3.91
3050 3569 7.365497 TCCATCTATGAGTTCATCTAAGCAA 57.635 36.000 0.00 0.00 37.76 3.91
3051 3570 7.212976 TCCATCTATGAGTTCATCTAAGCAAC 58.787 38.462 0.00 0.00 37.76 4.17
3052 3571 6.145209 CCATCTATGAGTTCATCTAAGCAACG 59.855 42.308 0.00 0.00 37.76 4.10
3053 3572 6.451064 TCTATGAGTTCATCTAAGCAACGA 57.549 37.500 0.00 0.00 37.76 3.85
3054 3573 6.499172 TCTATGAGTTCATCTAAGCAACGAG 58.501 40.000 0.00 0.00 37.76 4.18
3055 3574 4.521130 TGAGTTCATCTAAGCAACGAGT 57.479 40.909 0.00 0.00 0.00 4.18
3056 3575 4.486090 TGAGTTCATCTAAGCAACGAGTC 58.514 43.478 0.00 0.00 0.00 3.36
3057 3576 4.218635 TGAGTTCATCTAAGCAACGAGTCT 59.781 41.667 0.00 0.00 0.00 3.24
3058 3577 5.414765 TGAGTTCATCTAAGCAACGAGTCTA 59.585 40.000 0.00 0.00 0.00 2.59
3059 3578 5.885881 AGTTCATCTAAGCAACGAGTCTAG 58.114 41.667 0.00 0.00 0.00 2.43
3060 3579 4.902443 TCATCTAAGCAACGAGTCTAGG 57.098 45.455 0.00 0.00 0.00 3.02
3061 3580 3.632604 TCATCTAAGCAACGAGTCTAGGG 59.367 47.826 0.00 0.00 0.00 3.53
3062 3581 3.361281 TCTAAGCAACGAGTCTAGGGA 57.639 47.619 0.00 0.00 0.00 4.20
3063 3582 3.280295 TCTAAGCAACGAGTCTAGGGAG 58.720 50.000 0.00 0.00 0.00 4.30
3064 3583 2.217510 AAGCAACGAGTCTAGGGAGA 57.782 50.000 0.00 0.00 0.00 3.71
3065 3584 1.757682 AGCAACGAGTCTAGGGAGAG 58.242 55.000 0.00 0.00 30.20 3.20
3066 3585 1.282447 AGCAACGAGTCTAGGGAGAGA 59.718 52.381 0.00 0.00 30.20 3.10
3067 3586 1.673920 GCAACGAGTCTAGGGAGAGAG 59.326 57.143 0.00 0.00 30.20 3.20
3068 3587 2.942306 GCAACGAGTCTAGGGAGAGAGT 60.942 54.545 0.00 0.00 30.20 3.24
3069 3588 3.349022 CAACGAGTCTAGGGAGAGAGTT 58.651 50.000 0.00 0.00 30.20 3.01
3070 3589 3.724732 ACGAGTCTAGGGAGAGAGTTT 57.275 47.619 0.00 0.00 30.20 2.66
3071 3590 4.036941 ACGAGTCTAGGGAGAGAGTTTT 57.963 45.455 0.00 0.00 30.20 2.43
3072 3591 4.011698 ACGAGTCTAGGGAGAGAGTTTTC 58.988 47.826 0.00 0.00 30.20 2.29
3073 3592 4.011023 CGAGTCTAGGGAGAGAGTTTTCA 58.989 47.826 0.00 0.00 30.20 2.69
3074 3593 4.642885 CGAGTCTAGGGAGAGAGTTTTCAT 59.357 45.833 0.00 0.00 30.20 2.57
3075 3594 5.220970 CGAGTCTAGGGAGAGAGTTTTCATC 60.221 48.000 0.00 0.00 30.20 2.92
3076 3595 5.837829 AGTCTAGGGAGAGAGTTTTCATCT 58.162 41.667 0.00 0.00 30.20 2.90
3077 3596 6.975949 AGTCTAGGGAGAGAGTTTTCATCTA 58.024 40.000 0.00 0.00 30.20 1.98
3078 3597 6.831868 AGTCTAGGGAGAGAGTTTTCATCTAC 59.168 42.308 0.00 0.00 30.20 2.59
3079 3598 6.603997 GTCTAGGGAGAGAGTTTTCATCTACA 59.396 42.308 0.00 0.00 30.20 2.74
3080 3599 7.286775 GTCTAGGGAGAGAGTTTTCATCTACAT 59.713 40.741 0.00 0.00 30.20 2.29
3081 3600 8.503573 TCTAGGGAGAGAGTTTTCATCTACATA 58.496 37.037 0.00 0.00 0.00 2.29
3082 3601 7.354751 AGGGAGAGAGTTTTCATCTACATAC 57.645 40.000 0.00 0.00 0.00 2.39
3083 3602 6.325286 AGGGAGAGAGTTTTCATCTACATACC 59.675 42.308 0.00 0.00 0.00 2.73
3084 3603 6.098409 GGGAGAGAGTTTTCATCTACATACCA 59.902 42.308 0.00 0.00 0.00 3.25
3085 3604 6.981559 GGAGAGAGTTTTCATCTACATACCAC 59.018 42.308 0.00 0.00 0.00 4.16
3086 3605 7.147811 GGAGAGAGTTTTCATCTACATACCACT 60.148 40.741 0.00 0.00 0.00 4.00
3087 3606 8.140112 AGAGAGTTTTCATCTACATACCACTT 57.860 34.615 0.00 0.00 0.00 3.16
3088 3607 8.037758 AGAGAGTTTTCATCTACATACCACTTG 58.962 37.037 0.00 0.00 0.00 3.16
3089 3608 7.680730 AGAGTTTTCATCTACATACCACTTGT 58.319 34.615 0.00 0.00 0.00 3.16
3090 3609 8.812972 AGAGTTTTCATCTACATACCACTTGTA 58.187 33.333 0.00 0.00 0.00 2.41
3091 3610 9.088512 GAGTTTTCATCTACATACCACTTGTAG 57.911 37.037 4.81 4.81 45.12 2.74
3096 3615 5.434352 TCTACATACCACTTGTAGATCGC 57.566 43.478 8.96 0.00 46.52 4.58
3097 3616 3.079960 ACATACCACTTGTAGATCGCG 57.920 47.619 0.00 0.00 31.61 5.87
3098 3617 2.426024 ACATACCACTTGTAGATCGCGT 59.574 45.455 5.77 0.00 31.61 6.01
3099 3618 2.554806 TACCACTTGTAGATCGCGTG 57.445 50.000 5.77 0.00 0.00 5.34
3100 3619 0.736325 ACCACTTGTAGATCGCGTGC 60.736 55.000 5.77 0.00 0.00 5.34
3101 3620 1.625870 CACTTGTAGATCGCGTGCG 59.374 57.895 5.77 8.14 41.35 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
321 328 3.064207 GTCTGAGCGACACCACATAAAA 58.936 45.455 0.00 0.0 42.37 1.52
365 373 1.737793 CGACACCACATAAAGGGCTTC 59.262 52.381 0.00 0.0 0.00 3.86
565 575 5.914635 ACTTTGAATGTACTCGCAAACATTG 59.085 36.000 11.98 0.0 44.27 2.82
623 633 4.020573 TCCTCTCCGTGCAAGAAAAATCTA 60.021 41.667 0.00 0.0 0.00 1.98
1127 1141 6.042143 ACAAAAACTTGTTCAAATCGAGCAT 58.958 32.000 0.00 0.0 34.49 3.79
1187 1202 1.833630 TCAGCAAGACCCTCGAATGAT 59.166 47.619 0.00 0.0 0.00 2.45
1429 1472 7.276218 CCCTGCAATACAAAAATTCAGTACATG 59.724 37.037 0.00 0.0 0.00 3.21
1433 1632 6.266558 ACACCCTGCAATACAAAAATTCAGTA 59.733 34.615 0.00 0.0 0.00 2.74
1716 1916 4.096231 CCACACACACTGAAATGTTCTCAA 59.904 41.667 0.00 0.0 0.00 3.02
2135 2357 9.764363 CCATAGCTAGTACAAAAGACATCATTA 57.236 33.333 0.00 0.0 0.00 1.90
2266 2529 6.608539 TGTTAGTATGCCAGGTACAAACTA 57.391 37.500 0.00 0.0 0.00 2.24
2474 2962 7.241376 TCGTCAAAAGAAGAAAAAGTTCAGTC 58.759 34.615 0.00 0.0 36.09 3.51
2493 2981 4.634004 ACATGTTGTCTTCAGTTTCGTCAA 59.366 37.500 0.00 0.0 0.00 3.18
2749 3253 0.729478 CGACGACGAGCTTGATGTGT 60.729 55.000 8.31 0.0 42.66 3.72
2757 3261 2.820479 CTCCTCCGACGACGAGCT 60.820 66.667 9.28 0.0 42.66 4.09
2806 3310 1.065345 CCTCCTACTCCTCTGACGACA 60.065 57.143 0.00 0.0 0.00 4.35
2975 3494 0.394488 TTCTGCAACGTTCCCCAACA 60.394 50.000 0.00 0.0 32.14 3.33
2976 3495 0.741915 TTTCTGCAACGTTCCCCAAC 59.258 50.000 0.00 0.0 0.00 3.77
2977 3496 1.475403 TTTTCTGCAACGTTCCCCAA 58.525 45.000 0.00 0.0 0.00 4.12
2978 3497 1.698506 ATTTTCTGCAACGTTCCCCA 58.301 45.000 0.00 0.0 0.00 4.96
2979 3498 2.812358 AATTTTCTGCAACGTTCCCC 57.188 45.000 0.00 0.0 0.00 4.81
2980 3499 6.779115 ATTTTAATTTTCTGCAACGTTCCC 57.221 33.333 0.00 0.0 0.00 3.97
2981 3500 9.497030 AAAAATTTTAATTTTCTGCAACGTTCC 57.503 25.926 12.19 0.0 45.16 3.62
2983 3502 9.497030 GGAAAAATTTTAATTTTCTGCAACGTT 57.503 25.926 12.19 0.0 45.16 3.99
2984 3503 8.888716 AGGAAAAATTTTAATTTTCTGCAACGT 58.111 25.926 12.19 0.0 45.16 3.99
3014 3533 7.396540 ACTCATAGATGGATTTTGGTGAAAC 57.603 36.000 0.00 0.0 0.00 2.78
3015 3534 7.669304 TGAACTCATAGATGGATTTTGGTGAAA 59.331 33.333 0.00 0.0 0.00 2.69
3016 3535 7.174413 TGAACTCATAGATGGATTTTGGTGAA 58.826 34.615 0.00 0.0 0.00 3.18
3017 3536 6.720309 TGAACTCATAGATGGATTTTGGTGA 58.280 36.000 0.00 0.0 0.00 4.02
3018 3537 7.501559 AGATGAACTCATAGATGGATTTTGGTG 59.498 37.037 0.00 0.0 36.57 4.17
3019 3538 7.580910 AGATGAACTCATAGATGGATTTTGGT 58.419 34.615 0.00 0.0 36.57 3.67
3020 3539 9.565090 TTAGATGAACTCATAGATGGATTTTGG 57.435 33.333 0.00 0.0 36.57 3.28
3022 3541 9.282569 GCTTAGATGAACTCATAGATGGATTTT 57.717 33.333 0.00 0.0 36.57 1.82
3023 3542 8.435187 TGCTTAGATGAACTCATAGATGGATTT 58.565 33.333 0.00 0.0 36.57 2.17
3024 3543 7.971201 TGCTTAGATGAACTCATAGATGGATT 58.029 34.615 0.00 0.0 36.57 3.01
3025 3544 7.550597 TGCTTAGATGAACTCATAGATGGAT 57.449 36.000 0.00 0.0 36.57 3.41
3026 3545 6.983906 TGCTTAGATGAACTCATAGATGGA 57.016 37.500 0.00 0.0 36.57 3.41
3027 3546 6.145209 CGTTGCTTAGATGAACTCATAGATGG 59.855 42.308 0.00 0.0 36.57 3.51
3028 3547 6.920210 TCGTTGCTTAGATGAACTCATAGATG 59.080 38.462 0.00 0.0 36.57 2.90
3029 3548 7.043961 TCGTTGCTTAGATGAACTCATAGAT 57.956 36.000 0.00 0.0 36.57 1.98
3030 3549 6.095580 ACTCGTTGCTTAGATGAACTCATAGA 59.904 38.462 0.00 0.0 36.57 1.98
3031 3550 6.269315 ACTCGTTGCTTAGATGAACTCATAG 58.731 40.000 0.00 0.0 36.57 2.23
3032 3551 6.095580 AGACTCGTTGCTTAGATGAACTCATA 59.904 38.462 0.00 0.0 36.57 2.15
3033 3552 5.078411 ACTCGTTGCTTAGATGAACTCAT 57.922 39.130 0.00 0.0 39.70 2.90
3034 3553 4.218635 AGACTCGTTGCTTAGATGAACTCA 59.781 41.667 0.00 0.0 0.00 3.41
3035 3554 4.739195 AGACTCGTTGCTTAGATGAACTC 58.261 43.478 0.00 0.0 0.00 3.01
3036 3555 4.792521 AGACTCGTTGCTTAGATGAACT 57.207 40.909 0.00 0.0 0.00 3.01
3037 3556 5.038033 CCTAGACTCGTTGCTTAGATGAAC 58.962 45.833 0.00 0.0 0.00 3.18
3038 3557 4.098044 CCCTAGACTCGTTGCTTAGATGAA 59.902 45.833 0.00 0.0 0.00 2.57
3039 3558 3.632604 CCCTAGACTCGTTGCTTAGATGA 59.367 47.826 0.00 0.0 0.00 2.92
3040 3559 3.632604 TCCCTAGACTCGTTGCTTAGATG 59.367 47.826 0.00 0.0 0.00 2.90
3041 3560 3.886505 CTCCCTAGACTCGTTGCTTAGAT 59.113 47.826 0.00 0.0 0.00 1.98
3042 3561 3.054582 TCTCCCTAGACTCGTTGCTTAGA 60.055 47.826 0.00 0.0 0.00 2.10
3043 3562 3.280295 TCTCCCTAGACTCGTTGCTTAG 58.720 50.000 0.00 0.0 0.00 2.18
3044 3563 3.054582 TCTCTCCCTAGACTCGTTGCTTA 60.055 47.826 0.00 0.0 0.00 3.09
3045 3564 2.096248 CTCTCCCTAGACTCGTTGCTT 58.904 52.381 0.00 0.0 0.00 3.91
3046 3565 1.282447 TCTCTCCCTAGACTCGTTGCT 59.718 52.381 0.00 0.0 0.00 3.91
3047 3566 1.673920 CTCTCTCCCTAGACTCGTTGC 59.326 57.143 0.00 0.0 0.00 4.17
3048 3567 2.993937 ACTCTCTCCCTAGACTCGTTG 58.006 52.381 0.00 0.0 0.00 4.10
3049 3568 3.724732 AACTCTCTCCCTAGACTCGTT 57.275 47.619 0.00 0.0 0.00 3.85
3050 3569 3.724732 AAACTCTCTCCCTAGACTCGT 57.275 47.619 0.00 0.0 0.00 4.18
3051 3570 4.011023 TGAAAACTCTCTCCCTAGACTCG 58.989 47.826 0.00 0.0 0.00 4.18
3052 3571 5.891551 AGATGAAAACTCTCTCCCTAGACTC 59.108 44.000 0.00 0.0 0.00 3.36
3053 3572 5.837829 AGATGAAAACTCTCTCCCTAGACT 58.162 41.667 0.00 0.0 0.00 3.24
3054 3573 6.603997 TGTAGATGAAAACTCTCTCCCTAGAC 59.396 42.308 0.00 0.0 0.00 2.59
3055 3574 6.732487 TGTAGATGAAAACTCTCTCCCTAGA 58.268 40.000 0.00 0.0 0.00 2.43
3056 3575 7.595819 ATGTAGATGAAAACTCTCTCCCTAG 57.404 40.000 0.00 0.0 0.00 3.02
3057 3576 7.506261 GGTATGTAGATGAAAACTCTCTCCCTA 59.494 40.741 0.00 0.0 0.00 3.53
3058 3577 6.325286 GGTATGTAGATGAAAACTCTCTCCCT 59.675 42.308 0.00 0.0 0.00 4.20
3059 3578 6.098409 TGGTATGTAGATGAAAACTCTCTCCC 59.902 42.308 0.00 0.0 0.00 4.30
3060 3579 6.981559 GTGGTATGTAGATGAAAACTCTCTCC 59.018 42.308 0.00 0.0 0.00 3.71
3061 3580 7.777095 AGTGGTATGTAGATGAAAACTCTCTC 58.223 38.462 0.00 0.0 0.00 3.20
3062 3581 7.726033 AGTGGTATGTAGATGAAAACTCTCT 57.274 36.000 0.00 0.0 0.00 3.10
3063 3582 7.819900 ACAAGTGGTATGTAGATGAAAACTCTC 59.180 37.037 0.00 0.0 0.00 3.20
3064 3583 7.680730 ACAAGTGGTATGTAGATGAAAACTCT 58.319 34.615 0.00 0.0 0.00 3.24
3065 3584 7.907214 ACAAGTGGTATGTAGATGAAAACTC 57.093 36.000 0.00 0.0 0.00 3.01
3076 3595 3.628942 ACGCGATCTACAAGTGGTATGTA 59.371 43.478 15.93 0.0 32.27 2.29
3077 3596 2.426024 ACGCGATCTACAAGTGGTATGT 59.574 45.455 15.93 0.0 34.81 2.29
3078 3597 2.789339 CACGCGATCTACAAGTGGTATG 59.211 50.000 15.93 0.0 0.00 2.39
3079 3598 2.798499 GCACGCGATCTACAAGTGGTAT 60.798 50.000 15.93 0.0 33.80 2.73
3080 3599 1.468565 GCACGCGATCTACAAGTGGTA 60.469 52.381 15.93 0.0 33.80 3.25
3081 3600 0.736325 GCACGCGATCTACAAGTGGT 60.736 55.000 15.93 0.0 33.80 4.16
3082 3601 1.742900 CGCACGCGATCTACAAGTGG 61.743 60.000 15.93 0.0 42.83 4.00
3083 3602 0.796870 TCGCACGCGATCTACAAGTG 60.797 55.000 15.93 0.0 44.01 3.16
3084 3603 1.504900 TCGCACGCGATCTACAAGT 59.495 52.632 15.93 0.0 44.01 3.16
3085 3604 4.377471 TCGCACGCGATCTACAAG 57.623 55.556 15.93 0.0 44.01 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.